Split Expression and Metadata into Reference (R), Subset (X), and Inference (Y) Sets — split_stratified_ancestry

Performs stratified sampling of an overrepresented group (X, e.g. EUR) to match the distribution of an underrepresented group (Y, e.g. AFR) based on a grouping variable (e.g., condition).

Usage

split_stratified_ancestry_sets(
  X,
  Y,
  MX,
  MY,
  g_col,
  a_col,
  seed = NULL,
  verbose = TRUE
)

Arguments

X: Numeric matrix or data.frame of features for cohort X; rows are samples and must align with MX.
Y: Numeric matrix or data.frame of features for cohort Y; rows are samples and must align with MY.
MX: Data.frame with metadata for X.
MY: Data.frame with metadata for Y.
g_col: Name of the metadata column holding the stratification label.
a_col: Name of the metadata column holding the ancestry label.
seed: Optional numeric seed for reproducibility of sampling.
verbose: Logical, whether to print messages.

Value

A list with the following elements (all matrices with rownames):

R: Reference set: remaining X after subsampling
X: Subset set: subsampled X matching Y
Y: Inference set: full Y, untouched
strata_info: list with usable/missing/insufficient strata